P-glycoprotein (Pgp) is a highly dynamic ATP-binding cassette (ABC) membrane transporter that effluxes a diversity of molecules out of cells. It is a major determinant of drug absorption, distribution, and excretion in intestines, liver, kidney and brain, and also an impediment to successful chemotherapy in some cancers, HIV and central nervous system (CNS) diseases. About half of marketed drugs are estimated to be transport substrates or inhibitors of Pgp, and the evaluation of Pgp susceptibility of drug candidates has become an important step in the development of new therapeutics in the pharmaceutical industry. However, Pgp binding molecules exhibit complex activities, acting as ATPase stimulators, inhibitors, transport substrates, or non- transportable ligands. Despite extensive studies, we still have very limited understanding of the mechanisms for the complex and polyspecific Pgp-drug interactions pertaining to Pgp transport, inhibition and evasion. This study aims to (1) define how structural and chemical properties of a ligand affect its interactions with Pgp, (2) characterize how Pgp reacts upon the binding of different classes of ligands, and (3) rationalize chemical synthesis to modify existing drugs to evade Pgp transport. We will use an integrative chemistry, structural and functional approach to tackle these aims, which is based on several major advances in the literature and that we have most recently made on Pgp structural determination and ligand interactions. First, we propose to conduct a thorough structure-activity relationship study within a focused library of ligands bearing common scaffolds. We will use a battery of functional assays, including ATPase activity, detailed drug binding and competition, cell-based transport, and drug resistance assays, as well as structural characterizations to evaluate these compounds. Second, we will use several complementary biophysical techniques, including X- ray crystallography, single particle electron microscopy (EM), and luminance resonance energy transfer (LRET), for the determination of Pgp/ligand complex structures, conformational distributions, and the kinetics of conformational changes. The characterization of Pgp conformations by EM and LRET, together with the screen of novel ligands, detergents and lipids, as well as new constructs to stabilize Pgp (and certain conformations), will facilitate higher resolution (< 3.0 ) structural studies, a critical barrier that has eluded Pgp thus far. Third, we will modify several Pgp drug substrates on positions that have been identified without diminution of drug potency, thus with a focus on resulting changes in Pgp interactions. By the related three aim studies we will achieve a detailed and fundamental understanding of polyspecific Pgp-drug interactions, which will have a far- reaching impact on drug discovery given the pharmacological and clinical significance of Pgp and that many current and investigational drugs are susceptible to Pgp efflux.